From 53ed60adfc35444ae9735c01a6b6100e8737532e Mon Sep 17 00:00:00 2001 From: "Huska, Matthew" Date: Wed, 6 Sep 2023 15:47:04 +0200 Subject: [PATCH] =?UTF-8?q?Update=20sublineage=20query=20for=20covsonar=20?= =?UTF-8?q?2,=20add=20warning=20note=1B[1~?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- faq.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/faq.md b/faq.md index 374ff8e..f0aae15 100644 --- a/faq.md +++ b/faq.md @@ -84,11 +84,13 @@ Semi-globally aligned Sequence: ATGCCATGATTAGGTGA-------- |Optimize sqlite database |`./sonar.py optimize --db test.db` |`sonar optimize --db test.db` | |Calculate database statistics |`./sonar.py info --db ${db}` |`sonar info --db test.db` | |Remove a set of sequences by ID |`./sonar.py remove --db test.db --file sequences-to-delete.ids` |`sonar delete --db test.db --sample-file sequences-to-delete.ids` | -|Identify sequences with a given lineage or any of its sublineages |`./sonar.py match --lineage B.1.1.7 --with-sublineage --db test.db --tsv` |`sonar match --db test.db --LINEAGE B.1.1.7 --with-sublineage LINEAGE` | +|Identify sequences with a given lineage or any of its sublineages |`./sonar.py match --lineage B.1.1.7 --with-sublineage --db test.db --tsv` |`sonar match --db test.db --LINEAGE "B.1.1.7*"` (see NOTE1 below!) | |Output all sequences, including purely ambiguous variations in profiles (e.g. N stretches)|`./sonar.py match --ambig --tsv --db test.db` |`sonar match --db test.db --showNX` | |Output all sequences that contain frameshift mutations |`./sonar.py match --only_frameshifts --db test.db` |`sonar match --db test.db --frameshifts-only` | |Output all sequences that do not belong to a given lineage, in a date range |`./sonar.py match --lineage ^B.1.1.529 --lineage ^BA.% --date 2021-12-01:2021-12-31 --db test.db --tsv` |`sonar match --db test.db --LINEAGE "^B.1.1.529" "^BA%" --DATE 2021-12-01:2021-12-31` | +NOTE1: Sublineage queries will not work if you have never run the `update-lineages` command on your database. Without that command, covSonar doesn't know the relationships between children and parent Pangolin lineages. + ## Troubleshooting **Q: `covSonar2` crashes with: `sqlite3.OperationalError: attempt to write a readonly database`**